Autoimmune encephalitis encompasses a group of immune mediated neuropsychiatric disorders charecterized by autoantibodies targeting synaptic receptors, ion channels or neuronal proteins such as NMDAR, AMPAR or neurexin, among others. The presence of autoantibodies in autoimmune encephalitis are a key feature for the diagnosis and treatment of the disorder. Therefore, they have become essential biomarkers with a high clinical value. However, the current variety of commercial diagnostic kits together with in-house methods, including cell lines, dissociated neurons or rodent brain tissue, is a major cause for discrepancy in the establishment of a defined diagnosis. Due to this lack of consensus in the criteria, the diagnosis of these autoimmune diseases become a challenging task. Additionally, for some of these autoantibodies their value as a biomarker is still questioned along with their pathogenicity. Thus, there is a need for the unification of assessment criteria and establishment of standardized protocols. This Methods Collection will include articles showing the diversity of methods used for routine screening, focusing on their advantages and disadvantages, as well as novel techniques to decrease the false positive or negative results or improve the sensitivity of the up-to-date tests. This will offer guidance and will largely contribute to the reproducibility and standardization of methods for the detection of these autoantibodies.